Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 66

System / cell line: sequences ✕ Assay: genbank ✕ Clear

ChimerDB 2.0--a knowledgebase for fusion genes updated.

PMID 19906715 · PMC2808913 · Nucleic acids research · 2010 · 8 claims · 4 setups

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ChimerDB 2.0 is an updated knowledgebase integrating fusion transcripts from GenBank transcriptome analysis with Sanger CGP, OMIM, PubMed, and Mitelman's database data.

genbank sra pubmed transcript-to-genome ngs literature
Kangaroo--a pattern-matching program for biological sequences.

PMID 12150718 · PMC119856 · BMC bioinformatics · 2002 · 7 claims · 2 setups

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Kangaroo is a web-based regular expression pattern-matching program that searches DNA, protein, or coding-region sequences across ten organisms with no restriction on query length or complexity.

coding regular-expression mutation
Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.

PMID 17931731 · PMC7114232 · Virus research · 2008 · 7 claims · 5 setups

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8 amino acid sites in the extracellular domain of hMPV lineage 1a show a higher rate of nonsynonymous than synonymous substitutions (posterior probability >0.95), indicating positive selection.

unique hmpv sequence neighbor-joining codon
ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

PMID 12493080 · PMC139979 · BMC bioinformatics · 2002 · 6 claims · 6 setups

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ORFer retrieves protein and nucleic acid sequences and annotations from NCBI GenBank using the XML sequence format

sequences parsed bacillus anopheles large-scale sequence orf
Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups

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Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function

species genomic jmjd6 jmjc reciprocal comparative est
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

est clustered sequences sequence est sequence orf
GenBank.

PMID 16381837 · PMC1347519 · Nucleic acids research · 2006 · 8 claims · 8 setups

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GenBank is a comprehensive public database of nucleotide sequences with supporting bibliographic and biological annotation, built and distributed by NCBI.

sapiens organisms genbank large-scale genome expressed blast
Bases and spaces: resources on the web for accessing the draft human genome.

PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

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By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

bac whole-genome draft submitted bac radiation initio
A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.

PMID 19852815 · PMC2771047 · BMC genomics · 2009 · 8 claims · 5 setups

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The Conditional Stepped Reciprocal Best Hit (CSRBH) approach, combining direct RBH and zebrafish-stepped RBH (SRBH), outperformed other ortholog assignment methods and attained 8,726 carp-human functional homolog relationships for 16,650 carp contigs

carp randomly zebrafish reciprocal sequence microarray
Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations.

PMID 16595074 · PMC3500179 · Human genomics · 2006 · 8 claims · 7 setups

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50 novel α-Gal A mutations were identified in 49 of 66 unrelated families with classic Fabry disease.

genomic α-gal cos-7 transcripts pcr southern microsatellite
Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals.

PMID 19889143 · PMC3032083 · Journal of viral hepatitis · 2010 · 7 claims · 8 setups

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O-HBV-associated mutations in PreS/S/polymerase regions likely contribute to undetectable HBsAg by interfering with serologic detection, altering antigen secretion, and/or decreasing replicative fitness

serum hbv full-length o-hbv nested phylogenetic quasispecies
Sequencing of 16S rRNA gene: a rapid tool for identification of Bacillus anthracis.

PMID 12396926 · PMC2730316 · Emerging infectious diseases · 2002 · 7 claims · 4 setups

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All 86 B. anthracis isolates tested share an identical 16S rRNA gene sequence, designated 16S type 6

bacillus clinical additional 16s nested comparative
A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

PMID 18925953 · PMC2580767 · BMC genetics · 2008 · 8 claims · 6 setups

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A 460–465 bp insertion is present in intron 4 of the Amel-Y locus in most Cetartiodactyla lineages (cetaceans and ruminants) but absent in pig

cetacea amel-y amel-x cetartiodactyla pcr sanger molecular
BIPASS: BioInformatics Pipeline Alternative Splicing Services.

PMID 17584795 · PMC1933140 · Nucleic acids research · 2007 · 8 claims · 4 setups

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BIPASS offers two complementary services for alternative splicing (AS) research: BIPAS-SpliceDB, a queryable pre-computed AS data warehouse, and BIPAS-Align&Splice, an online pipeline for user-submitted sequences.

transcript aligned pre-computed user-submitted sequence alternative database
The role of genomics in the identification, prediction, and prevention of biological threats.

PMID 19855827 · PMC2757898 · PLoS biology · 2009 · 8 claims · 5 setups

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Genomics should be used proactively, not just reactively, to build biopreparedness against biological threats

bacillus escherichia sars pandemic whole-genome pangenomic low-resolution
Analysis of virulence factors of Helicobacter pylori isolated from a Vietnamese population.

PMID 19698173 · PMC2739534 · BMC microbiology · 2009 · 8 claims · 5 setups

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Three distinct deletion patterns (39-bp, 18-bp, no deletion) exist upstream of the cagA EPIYA repeat region (pre-EPIYA region), providing a novel genotyping marker.

pylori gastric pcr sequence comparative
Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

PMID 18687142 · PMC2546438 · Retrovirology · 2008 · 7 claims · 6 setups

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Integrase displays significantly less inter- and intra-subtype amino acid diversity and lower Shannon's entropy than protease or RT.

genbank hiv-1 protease integrase blastp phylogenetic amino
ChimerDB--a knowledgebase for fusion sequences.

PMID 16381848 · PMC1347382 · Nucleic acids research · 2006 · 8 claims · 6 setups

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ChimerDB integrates bioinformatics analysis of mRNA/EST sequences, manually collected literature data, and OMIM translocation data into a single fusion sequence knowledgebase

genome candidate pubmed omim blat splice-site ecgene
Database resources of the National Center for Biotechnology Information.

PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups

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NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis

genbank genomic eukaryotic completely sequence rapid est
Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.

PMID 17386095 · PMC1868932 · Genome biology · 2007 · 8 claims · 4 setups

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More than 55,000 totally intronic noncoding (TIN) RNAs are transcribed from the introns of 74% of unique RefSeq genes.

dbest liver cultures refseq est oligoarray polymerase

Experiments

ChimerDB 2.0--a knowledgebase for fusion genes updated.

Kangaroo--a pattern-matching program for biological sequences.

Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.

ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

GenBank.

Bases and spaces: resources on the web for accessing the draft human genome.

A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.

Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations.

Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals.

Sequencing of 16S rRNA gene: a rapid tool for identification of Bacillus anthracis.

A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

BIPASS: BioInformatics Pipeline Alternative Splicing Services.

The role of genomics in the identification, prediction, and prevention of biological threats.

Analysis of virulence factors of Helicobacter pylori isolated from a Vietnamese population.

Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

ChimerDB--a knowledgebase for fusion sequences.

Database resources of the National Center for Biotechnology Information.

Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.